Nonrandom location of IS1 elements in the genomes of natural isolates of Escherichia coli

We have studied the spatial distribution of IS1 elements in the genomes ofnatural isolates comprising the ECOR reference collection of Escherichiacoli. We find evidence for nonrandomness at three levels. Many pairs of IS1elements are in much closer proximity (< 10 kb) than can be accountedfor by chance. IS1 elements in close proximity were identified bylong-range PCR amplification of the genomic sequence between them. Eachamplified region was sequenced and its map location determined by databasescreening of DNA hybridization. Among the ECOR strains with at least twoIS1 elements, 54% had one or more pairs of elements separated by < 10kb. We propose that this type of clustering is a result of "local hopping,"in which we assume that a significant proportion of tranposition eventsleads to the insertion of a daughter IS element in the vicinity of theparental element. A second level of nonrandomness is found in strains witha modest number of IS1 elements that are mapped through the use of inversePCR to amplify flanking genomic sequences: in these strains, the insertionsites tend to be clustered over a smaller region of chromosome than wouldbe expected by chance. A third level of nonrandomness is observed in thecomposite distribution of IS elements across strains: among 20 mapped IS1elements, none were found in the region of 48-77 minutes, a significantgap. One region of the E. coli chromosome, at 98 min, had a cluster of IS1elements in seven ECOR strains of diverse phylogenetic origin. We deducefrom sequence analysis that this pattern of distribution is a result ofinitial insertion in the most recent common ancestor of these strains andtherefore not a hot spot of insertion. Analysis using long- range PCR withprimers for IS2 and IS3 also yielded pairs of elements in close proximity,suggesting that these elements may also occasionally transpose by localhopping.